A hybrid membrane of sulfonated poly(ether ether ketone)/polydopamine-coated carbon nanotubes loaded phosphotungstic acid (S/DCNTs-HPW) is proposed for vanadium redox flow battery (VRFB). With the DCNTs-HPW nanofillers as the proton donor and acceptor, a high proton conductivity and low vanadium ions permeability of the S/DCNTs-HPW hybrid membranes is demonstrated owing to the formed acid-base interaction. Specifically, S/DCNTs-HPW-1 gives higher ion selectivity (25.4 × 103 S min cm−3) than that of pristine SPEEK (4.3 × 103 S min cm−3) and Nafion 117 (4.0 × 103 S min cm−3). Cell utilizing S/DCNTs-HPW-1 reveals excellent coulombic efficiency (98.2–99.4%) and energy efficiency (89.5–69.0%) under the current density of 50–160 mA cm−2, and a 34.5% charge capacity retention under 100 cycles is achieved based on the excellent membrane structure and chemical stability. The S/DCNTs-HPW-1 membrane shows a self-discharge time of 576 h, which is longer than that of the Nafion 117 membrane (23 h). Thus, the S/DCNTs-HPW hybrid membranes are suggested for potential use as alternative PEMs in the VRFB system.